Structure of λ CII: Implications for recognition of direct-repeat DNA by an unusual tetrameric organization

doi:10.1073/pnas.0504535102

Structure of λ CII: Implications for recognition of direct-repeat DNA by an unusual tetrameric organization

^*Department of Biochemistry, Bose Institute, P1/12 CIT Scheme VIIM, Calcutta 700 054, India; and ^†European Molecular Biology Laboratory, Hamburg Outstation, c/o Deutsches Elektronen Synchrotron, 22603 Hamburg, Germany

Communicated by Allan M. Campbell, Stanford University, Stanford, CA, June 20, 2005 (received for review February 21, 2005)

Abstract

The temperate coliphage λ, after infecting its host bacterium Escherichia coli, can develop either along the lytic or the lysogenic pathway. Crucial to the lysis/lysogeny decision is the homotetrameric transcription-activator protein CII (4 × 11 kDa) of the phage that binds to a unique direct-repeat sequence T-T-G-C-N₆-T-T-G-C at each of the three phage promoters it activates: p _E, p _I, and p _aQ. Several regions of CII have been identified for its various functions (DNA binding, oligomerization, and susceptibility to host protease), but the crystal structure of the protein long remained elusive. Here, we present the three-dimensional structure of CII at 2.6-Å resolution. The CII monomer is comprised of four α helices and a disordered C terminus. The first three helices (α1–α3) form a compact domain, whereas the fourth helix (α4) protrudes in different orientations in each subunit. A four-helix bundle, formed by α4 from each subunit, holds the tetramer. The quaternary structure can be described as a dimer of dimers, but the tetramer does not exhibit a closed symmetry. This unusual quaternary arrangement allows the placement of the helix–turn–helix motifs of two of the four CII subunits for interaction with successive major grooves of B-DNA, from one face of DNA. This structure provides a simple explanation for how a homotetrameric protein may recognize a direct-repeat DNA sequence rather than the inverted-repeat sequences of most prokaryotic activators.

Footnotes

↵ § To whom correspondence may be addressed. E-mail: pradeep{at}bic.boseinst.ernet.in or pinak{at}bic.boseinst.ernet.in.
↵ ‡ Present address: Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14850.
Author contributions: A.B.D., P.C., and P.P. designed research; A.B.D. and S.P. performed research; M.S.W. contributed new reagents/analytic tools; A.B.D., S.P., M.S.W., P.C., and P.P. analyzed data; and A.B.D., P.C., and P.P. wrote the paper.
Abbreviations: HTH, helix–turn–helix; MAD, multiple-wavelength anomalous dispersion.
Data deposition: The atomic coordinates and structure factors have been deposited in the Protein Data Bank, www.pdb.org (PDB ID code 1XWR).